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Yu D, Liu J, Chen Y. Do not ignore another risk factor of invasive fungal infections in patients with connective tissue disease. Semin Arthritis Rheum 2024; 65:152393. [PMID: 38330739 DOI: 10.1016/j.semarthrit.2024.152393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 01/26/2024] [Indexed: 02/10/2024]
Affiliation(s)
- Diao Yu
- Department of Clinical Laboratory, Zhejiang Provincial People's Hospital Bijie Hospital, Bijie, Guizhou, China
| | - Jinlin Liu
- Department of Clinical Laboratory, South China Hospital, Medical School, Shenzhen University, Shenzhen, China.
| | - Yanxia Chen
- Department of Rheumatology and Immunology, South China Hospital, Medical School, Shenzhen University, 1 Fuxin Road, Shenzhen 518111, China.
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Rao M, Mikdashi J. A Framework to Overcome Challenges in the Management of Infections in Patients with Systemic Lupus Erythematosus. Open Access Rheumatol 2023; 15:125-137. [PMID: 37534019 PMCID: PMC10391536 DOI: 10.2147/oarrr.s295036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023] Open
Abstract
Infections remain one of the leading causes of death in systemic lupus erythematosus (SLE), despite awareness of factors contributing to increased susceptibility to infectious diseases in SLE. Clinicians report challenges and barriers when encountering infection in SLE as certain infections may mimic a lupus flare. There are no evidence-based practice guidelines in the management of fever in SLE, with suboptimal implementations of evidence-based benefits related to infectious disease control and/or prevention strategies in SLE. Vigilance in identifying an opportunistic infection must be stressed when confronted by a diagnostic challenge during a presentation with a febrile illness in SLE. A balanced approach must focus on management of infections in SLE, and reduction in the glucocorticoids dose, given the need to control lupus disease activity to avoid lupus related organ damage and mortality. Clinical judgement and application of biomarkers of lupus flares could reduce false positives and overdiagnosis and improve differentiation of infections from lupus flares. Further precision-based risk and screening measures must identify individuals who would benefit most from low dose immunosuppressive therapy, targeted immune therapy, and vaccination programs.
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Affiliation(s)
- Madhavi Rao
- Department of Medicine, Division of Rheumatology and Clinical Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jamal Mikdashi
- Department of Medicine, Division of Rheumatology and Clinical Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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Deng T, Chen S, Zhang Y, Xu Y, Feng D, Wu H, Sun X. A cofunctional grouping-based approach for non-redundant feature gene selection in unannotated single-cell RNA-seq analysis. Brief Bioinform 2023; 24:bbad042. [PMID: 36754847 PMCID: PMC10025445 DOI: 10.1093/bib/bbad042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/05/2022] [Accepted: 01/18/2023] [Indexed: 02/10/2023] Open
Abstract
Feature gene selection has significant impact on the performance of cell clustering in single-cell RNA sequencing (scRNA-seq) analysis. A well-rounded feature selection (FS) method should consider relevance, redundancy and complementarity of the features. Yet most existing FS methods focus on gene relevance to the cell types but neglect redundancy and complementarity, which undermines the cell clustering performance. We develop a novel computational method GeneClust to select feature genes for scRNA-seq cell clustering. GeneClust groups genes based on their expression profiles, then selects genes with the aim of maximizing relevance, minimizing redundancy and preserving complementarity. It can work as a plug-in tool for FS with any existing cell clustering method. Extensive benchmark results demonstrate that GeneClust significantly improve the clustering performance. Moreover, GeneClust can group cofunctional genes in biological process and pathway into clusters, thus providing a means of investigating gene interactions and identifying potential genes relevant to biological characteristics of the dataset. GeneClust is freely available at https://github.com/ToryDeng/scGeneClust.
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Affiliation(s)
- Tao Deng
- School of Data Science, The Chinese University of Hong Kong—Shenzhen, Guangdong, China
| | - Siyu Chen
- School of Statistics and Mathematics, Zhongnan University of Economics and Law, Hubei, China
| | - Ying Zhang
- School of Statistics and Mathematics, Zhongnan University of Economics and Law, Hubei, China
| | - Yuanbin Xu
- School of Statistics and Mathematics, Zhongnan University of Economics and Law, Hubei, China
| | - Da Feng
- School of Pharmacy, Tongji Medical College, Huazhong University of Sciences and Technology, Hubei, China
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, GA, USA
- Faculty of Computer Science and Control Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Xiaobo Sun
- School of Statistics and Mathematics, Zhongnan University of Economics and Law, Hubei, China
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Ling Z, Cheng Y, Gao J, Lei W, Yan X, Hu X, Shao L, Liu X, Kang R. Alterations of the fecal and vaginal microbiomes in patients with systemic lupus erythematosus and their associations with immunological profiles. Front Immunol 2023; 14:1135861. [PMID: 36969178 PMCID: PMC10036376 DOI: 10.3389/fimmu.2023.1135861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
BackgroundExploring the human microbiome in multiple body niches is beneficial for clinicians to determine which microbial dysbiosis should be targeted first. We aimed to study whether both the fecal and vaginal microbiomes are disrupted in SLE patients and whether they are correlated, as well as their associations with immunological features.MethodsA group of 30 SLE patients and 30 BMI-age-matched healthy controls were recruited. Fecal and vaginal samples were collected, the 16S rRNA gene was sequenced to profile microbiomes, and immunological features were examined.ResultsDistinct fecal and vaginal bacterial communities and decreased microbial diversity in feces compared with the vagina were found in SLE patients and controls. Altered bacterial communities were found in the feces and vaginas of patients. Compared with the controls, the SLE group had slightly lower gut bacterial diversity, which was accompanied by significantly higher bacterial diversity in their vaginas. The most predominant bacteria differed between feces and the vagina in all groups. Eleven genera differed in patients’ feces; for example, Gardnerella and Lactobacillus increased, whereas Faecalibacterium decreased. Almost all the 13 genera differed in SLE patients’ vaginas, showing higher abundances except for Lactobacillus. Three genera in feces and 11 genera in the vagina were biomarkers for SLE patients. The distinct immunological features were only associated with patients’ vaginal microbiomes; for example, Escherichia−Shigella was negatively associated with serum C4.ConclusionsAlthough SLE patients had fecal and vaginal dysbiosis, dysbiosis in the vagina was more obvious than that in feces. Additionally, only the vaginal microbiome interacted with patients’ immunological features.
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Affiliation(s)
- Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
- *Correspondence: Zongxin Ling, ; Runfang Kang,
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jie Gao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wenhui Lei
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Xiumei Yan
- Department of Geriatrics, Lishui Second People’s Hospital, Lishui, Zhejiang, China
| | - Xiaogang Hu
- Department of Geriatrics, Lishui Second People’s Hospital, Lishui, Zhejiang, China
| | - Li Shao
- School of Clinical Medicine, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xia Liu
- Department of Intensive Care Unit, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Runfang Kang
- Department of Dermatology, Lishui Second People’s Hospital, Lishui, Zhejiang, China
- *Correspondence: Zongxin Ling, ; Runfang Kang,
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Romero-Ramírez S, Sosa-Hernández VA, Cervantes-Díaz R, Carrillo-Vázquez DA, Meza-Sánchez DE, Núñez-Álvarez C, Torres-Ruiz J, Gómez-Martín D, Maravillas-Montero JL. Salivary IgA subtypes as novel disease biomarkers in systemic lupus erythematosus. Front Immunol 2023; 14:1080154. [PMID: 36911711 PMCID: PMC9992540 DOI: 10.3389/fimmu.2023.1080154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction Immunoglobulin A (IgA) is the main antibody isotype in body fluids such as tears, intestinal mucous, colostrum, and saliva. There are two subtypes of IgA in humans: IgA1, mainly present in blood and mucosal sites, and IgA2, preferentially expressed in mucosal sites like the colon. In clinical practice, immunoglobulins are typically measured in venous or capillary blood; however, alternative samples, including saliva, are now being considered, given their non-invasive and easy collection nature. Several autoimmune diseases have been related to diverse abnormalities in oral mucosal immunity, such as rheumatoid arthritis, Sjogren's syndrome, and systemic lupus erythematosus (SLE). Methods We decided to evaluate the levels of both IgA subtypes in the saliva of SLE patients. A light chain capture-based ELISA measured specific IgA1 and IgA2 levels in a cohort of SLE patients compared with age and gender-matched healthy volunteers. Results Surprisingly, our results indicated that in the saliva of SLE patients, total IgA and IgA1 subtype were significantly elevated; we also found that salivary IgA levels, particularly IgA2, positively correlate with anti-dsDNA IgG antibody titers. Strikingly, we also detected the presence of salivary anti-nucleosome IgA antibodies in SLE patients, a feature not previously reported elsewhere. Conclusions According to our results and upon necessary validation, IgA characterization in saliva could represent a potentially helpful tool in the clinical care of SLE patients with the advantage of being a more straightforward, faster, and safer method than manipulating blood samples.
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Affiliation(s)
- Sandra Romero-Ramírez
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.,Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Víctor A Sosa-Hernández
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.,Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Rodrigo Cervantes-Díaz
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.,Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniel A Carrillo-Vázquez
- Departamento de Medicina Interna, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - David E Meza-Sánchez
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Carlos Núñez-Álvarez
- Departamento de Inmunología y Reumatología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Jiram Torres-Ruiz
- Departamento de Inmunología y Reumatología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Diana Gómez-Martín
- Departamento de Inmunología y Reumatología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - José L Maravillas-Montero
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
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Naik B, Rana R, Yadav M, Singh U, Singh A, Singh S. Serum complements and immunoglobulin profiles in systemic lupus erythematosus patients: An observational study at a teaching hospital. J Family Med Prim Care 2022; 11:608-613. [PMID: 35360789 PMCID: PMC8963632 DOI: 10.4103/jfmpc.jfmpc_960_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 11/04/2022] Open
Abstract
Context: Serum complement proteins and autoantibodies play an important role in the pathogenesis and diagnosis of systemic lupus erythematosus (SLE). Abnormalities in various immunoglobulin levels are described in patients of SLE. Aims: To study the spectrum of clinical manifestations and measure the serum levels of complement C3, complement C4, autoantibodies and immunoglobulin G (IgG) in patients of SLE and compare with healthy controls. Settings and Design: The present study is a prospective hospital-based observational study conducted between May 2014 and December 2018. Statistical Analysis Used: Unpaired t-test was used to compare the mean values between the SLE patients and healthy controls. Material and Methods: A total of 100 cases of SLE and 100 healthy controls were included in the study. The clinical data were retrieved. Serum antinuclear antibody, anti-ds DNA antibody, and anti-Smith antibody levels, and complements C3, C4 and IgG were measured. Results: Arthritis (89%) and anaemia (65%) were two common clinical presentations. The low complement C3 levels and C4 were detected in 64 and 62% of the SLE patients. Serum IgG was increased in 41% of the patients. A reduced level of IgG was detected in 6% of the patients. Conclusion: Primary care physicians should be aware of the clinical and serological manifestations of SLE as early detection will reduce end-organ damage. Autoantibody testing and complement testing should be done in all suspected cases. This study showed a significantly reduced C3 and C4 and elevated IgG in many cases of SLE as compared to control. Hypogammaglobulinemia was also present in a minority of the cases.
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